Updating changes in human gut microbial communities associated with Clostridioides difficile infection.

Clostridioides difficile is the causative agent of antibiotic-associated diarrhea, a worldwide public health problem. Different factors can promote the progression of C. difficile infection (CDI), mainly altered intestinal microbiota composition. Microbial species belonging to different domains (i.e., bacteria, archaea, eukaryotes, and even viruses) are synergistically and antagonistically associated with CDI. This review was aimed at updating changes regarding CDI-related human microbiota composition using recent data and an integral approach that included the different microorganism domains. The three domains of life contribute to intestinal microbiota homeostasis at different levels in which relationships among microorganisms could explain the wide range of clinical manifestations. A holistic understanding of intestinal ecosystem functioning will facilitate identifying new predictive factors for infection and developing better treatment and new diagnostic tools, thereby reducing this disease's morbidity and mortality.

The rise of algae in Cryogenian oceans and the emergence of animals.

The transition from dominant bacterial to eukaryotic marine primary productivity was one of the most profound ecological revolutions in the Earth's history, reorganizing the distribution of carbon and nutrients in the water column and increasing energy flow to higher trophic levels. But the causes and geological timing of this transition, as well as possible links with rising atmospheric oxygen levels and the evolution of animals, remain obscure. Here we present a molecular fossil record of eukaryotic steroids demonstrating that bacteria were the only notable primary producers in the oceans before the Cryogenian period (720-635 million years ago). Increasing steroid diversity and abundance marks the rapid rise of marine planktonic algae (Archaeplastida) in the narrow time interval between the Sturtian and Marinoan 'snowball Earth' glaciations, 659-645 million years ago. We propose that the incumbency of cyanobacteria was broken by a surge of nutrients supplied by the Sturtian deglaciation. The 'Rise of Algae' created food webs with more efficient nutrient and energy transfers, driving ecosystems towards larger and increasingly complex organisms. This effect is recorded by the concomitant appearance of biomarkers for sponges and predatory rhizarians, and the subsequent radiation of eumetazoans in the Ediacaran period.

Validation of the Hirst-Type Spore Trap for Simultaneous Monitoring of Prokaryotic and Eukaryotic Biodiversities in Urban Air Samples by Next-Generation Sequencing.

Pollen, fungi, and bacteria are the main microscopic biological entities present in outdoor air, causing allergy symptoms and disease transmission and having a significant role in atmosphere dynamics. Despite their relevance, a method for monitoring simultaneously these biological particles in metropolitan environments has not yet been developed. Here, we assessed the use of the Hirst-type spore trap to characterize the global airborne biota by high-throughput DNA sequencing, selecting regions of the 16S rRNA gene and internal transcribed spacer for the taxonomic assignment. We showed that aerobiological communities are well represented by this approach. The operational taxonomic units (OTUs) of two traps working synchronically compiled >87% of the total relative abundance for bacterial diversity collected in each sampler, >89% for fungi, and >97% for pollen. We found a good correspondence between traditional characterization by microscopy and genetic identification, obtaining more-accurate taxonomic assignments and detecting a greater diversity using the latter. We also demonstrated that DNA sequencing accurately detects differences in biodiversity between samples. We concluded that high-throughput DNA sequencing applied to aerobiological samples obtained with Hirst spore traps provides reliable results and can be easily implemented for monitoring prokaryotic and eukaryotic entities present in the air of urban areas.IMPORTANCE Detection, monitoring, and characterization of the wide diversity of biological entities present in the air are difficult tasks that require time and expertise in different disciplines. We have evaluated the use of the Hirst spore trap (an instrument broadly employed in aerobiological studies) to detect and identify these organisms by DNA-based analyses. Our results showed a consistent collection of DNA and a good concordance with traditional methods for identification, suggesting that these devices can be used as a tool for continuous monitoring of the airborne biodiversity, improving taxonomic resolution and characterization together. They are also suitable for acquiring novel DNA amplicon-based information in order to gain a better understanding of the biological particles present in a scarcely known environment such as the air.

Composition and dynamics of biostimulated indigenous oil-degrading microbial consortia from the Irish, North and Mediterranean Seas: a mesocosm study.

Diversity of indigenous microbial consortia and natural occurrence of obligate hydrocarbon-degrading bacteria (OHCB) are of central importance for efficient bioremediation techniques. To investigate the microbial population dynamics and composition of oil-degrading consortia, we have established a series of identical oil-degrading mesocosms at three different locations, Bangor (Menai Straits, Irish Sea), Helgoland (North Sea) and Messina (Messina Straits, Mediterranean Sea). Changes in microbial community composition in response to oil spiking, nutrient amendment and filtration were assessed by ARISA and DGGE fingerprinting and 16Sr RNA gene library analysis. Bacterial and protozoan cell numbers were quantified by fluorescence microscopy. Very similar microbial population sizes and dynamics, together with key oil-degrading microorganisms, for example, Alcanivorax borkumensis, were observed at all three sites; however, the composition of microbial communities was largely site specific and included variability in relative abundance of OHCB. Reduction in protozoan grazing had little effect on prokaryotic cell numbers but did lead to a decrease in the percentage of A. borkumensis 16S rRNA genes detected in clone libraries. These results underline the complexity of marine oil-degrading microbial communities and cast further doubt on the feasibility of bioaugmentation practices for use in a broad range of geographical locations.

Earth's earliest non-marine eukaryotes.

The existence of a terrestrial Precambrian (more than 542 Myr ago) biota has been largely inferred from indirect chemical and geological evidence associated with palaeosols, the weathering of clay minerals and microbially induced sedimentary structures in siliciclastic sediments. Direct evidence of fossils within rocks of non-marine origin in the Precambrian is exceedingly rare. The most widely cited example comprises a single report of morphologically simple mineralized tubes and spheres interpreted as cyanobacteria, obtained from 1,200-Myr-old palaeokarst in Arizona. Organic-walled microfossils were first described from the non-marine Torridonian (1.2-1.0 Gyr ago) sequence of northwest Scotland in 1907. Subsequent studies found few distinctive taxa-a century later, the Torridonian microflora is still being characterized as primarily nondescript "leiospheres". We have comprehensively sampled grey shales and phosphatic nodules throughout the Torridonian sequence. Here we report the recovery of large populations of diverse organic-walled microfossils extracted by acid maceration, complemented by studies using thin sections of phosphatic nodules that yield exceptionally detailed three-dimensional preservation. These assemblages contain multicellular structures, complex-walled cysts, asymmetric organic structures, and dorsiventral, compressed organic thalli, some approaching one millimetre in diameter. They offer direct evidence of eukaryotes living in freshwater aquatic and subaerially exposed habitats during the Proterozoic era. The apparent dominance of eukaryotes in non-marine settings by 1 Gyr ago indicates that eukaryotic evolution on land may have commenced far earlier than previously thought.

An early Ediacaran assemblage of macroscopic and morphologically differentiated eukaryotes.

The deep-water Avalon biota (about 579 to 565 million years old) is often regarded as the earliest-known fossil assemblage with macroscopic and morphologically complex life forms. It has been proposed that the rise of the Avalon biota was triggered by the oxygenation of mid-Ediacaran deep oceans. Here we report a diverse assemblage of morphologically differentiated benthic macrofossils that were preserved largely in situ as carbonaceous compressions in black shales of the Ediacaran Lantian Formation (southern Anhui Province, South China). The Lantian biota, probably older than and taxonomically distinct from the Avalon biota, suggests that morphological diversification of macroscopic eukaryotes may have occurred in the early Ediacaran Period, perhaps shortly after the Marinoan glaciation, and that the redox history of Ediacaran oceans was more complex than previously thought.

18S rDNA sequences from microeukaryotes reveal oil indicators in mangrove sediment.

BACKGROUND: Microeukaryotes are an effective indicator of the presence of environmental contaminants. However, the characterisation of these organisms by conventional tools is often inefficient, and recent molecular studies have revealed a great diversity of microeukaryotes. The full extent of this diversity is unknown, and therefore, the distribution, ecological role and responses to anthropogenic effects of microeukaryotes are rather obscure. The majority of oil from oceanic oil spills (e.g., the May 2010 accident in the Gulf of Mexico) converges on coastal ecosystems such as mangroves, which are threatened with worldwide disappearance, highlighting the need for efficient tools to indicate the presence of oil in these environments. However, no studies have used molecular methods to assess the effects of oil contamination in mangrove sediment on microeukaryotes as a group. METHODOLOGY/PRINCIPAL FINDINGS: We evaluated the population dynamics and the prevailing 18S rDNA phylotypes of microeukaryotes in mangrove sediment microcosms with and without oil contamination, using PCR/DGGE and clone libraries. We found that microeukaryotes are useful for monitoring oil contamination in mangroves. Our clone library analysis revealed a decrease in both diversity and species richness after contamination. The phylogenetic group that showed the greatest sensitivity to oil was the Nematoda. After contamination, a large increase in the abundance of the groups Bacillariophyta (diatoms) and Biosoecida was detected. The oil-contaminated samples were almost entirely dominated by organisms related to Bacillariophyta sp. and Cafeteria minima, which indicates that these groups are possible targets for biomonitoring oil in mangroves. The DGGE fingerprints also indicated shifts in microeukaryote profiles; specific band sequencing indicated the appearance of Bacillariophyta sp. only in contaminated samples and Nematoda only in non-contaminated sediment. CONCLUSIONS/SIGNIFICANCE: We believe that the microeukaryotic targets indicated by our work will be of great applicability in biomonitoring hydrocarbons in mangroves under oil contamination risk or during recovery strategies.

Bacterial and protozoal communities and fatty acid profile in the rumen of sheep fed a diet containing added tannins.

This study evaluated the effects of tannins on ruminal biohydrogenation (BH) due to shifts in the ruminal microbial environment in sheep. Thirteen lambs (45 days of age) were assigned to two dietary treatments: seven lambs were fed a barley-based concentrate (control group) while the other six lambs received the same concentrate with supplemental quebracho tannins (9.57% of dry matter). At 122 days of age, the lambs were slaughtered, and the ruminal contents were subjected to fatty acid analysis and sampled to quantify populations of Butyrivibrio fibrisolvens, which converts C(18:2) c9-c12 (linoleic acid [LA]) to C(18:2) c9-t11 (rumenic acid [RA]) and then RA to C(18:1) t11 (vaccenic acid [VA]); we also sampled for Butyrivibrio proteoclasticus, which converts VA to C(18:0) (stearic acid [SA]). Tannins increased (P < 0.005) VA in the rumen compared to the tannin-free diet. The concentration of SA was not affected by tannins. The SA/VA ratio was lower (P < 0.005) for the tannin-fed lambs than for the controls, suggesting that the last step of the BH process was inhibited by tannins. The B. proteoclasticus population was lower (-30.6%; P < 0.1), and B. fibrisolvens and protozoan populations were higher (+107% and +56.1%, respectively; P < 0.05) in the rumen of lambs fed the tannin-supplemented diet than in controls. These results suggest that quebracho tannins altered BH by changing ruminal microbial populations.

Structure and composition of aggregates in two large European rivers, based on confocal laser scanning microscopy and image and statistical analyses.

Floating riverine aggregates are composed of a complex mixture of inorganic and organic components from their respective aquatic habitats. Their architecture and integrity are supplemented by the presence of extracellular polymeric substances of microbial origin. They are also a habitat for virus-like particles, bacteria, archaea, fungi, algae, and protozoa. In this study we present different confocal laser scanning microscopy strategies to examine aggregates collected from the Danube and Elbe Rivers. In order to collect multiple types of information, various approaches were necessary. Small aggregates were examined directly. To analyze large and dense aggregates, limitations of the technique were overcome by cryo-sectioning and poststaining of the samples. The staining procedure included positive staining (specific glycoconjugates and cellular nucleic acid signals) as well as negative staining (aggregate volume) and multichannel recording. Data sets of cellular nucleic acid signals (CNAS) and the structure of aggregates were visualized and quantified using digital image analysis. The Danube and Elbe Rivers differed in their aggregate composition and in the relative contribution of specific glycoconjugate and CNAS volume to the aggregate volume; these contributions also changed over time. We report different spatial patterns of CNAS inside riverine aggregates, depending on aggregate size and season. The spatial structure of CNAS inside riverine aggregates was more complex in the Elbe River than in the Danube River. Based on our samples, we discuss the strengths and challenges involved in scanning and quantifying riverine aggregates.

Changes in microbial community structure, methanogenesis and rumen fermentation in response to saponin-rich fractions from different plant materials.

AIMS: Investigation of the effects of saponin-rich fractions on rumen fermentation, methane production and the microbial community. METHODS AND RESULTS: Saponins were extracted from Carduus, Sesbania and Knautia leaves and fenugreek seeds. Two levels of saponin-rich fractions with a substrate were incubated using the Hohenheim gas method. Methane was measured using an infrared-based methane analyser and microbial communities using quantitative PCR. On addition of saponin-rich fractions, methane and short-chain fatty acid production was not affected. The protozoal counts decreased by 10-39%. Sesbania saponins decreased methanogen population by 78%. Decrease in ruminal fungal population (20-60%) and increase in Fibrobacter succinogenes (21-45%) and Ruminococcus flavefaciens (23-40%) were observed. CONCLUSIONS: The saponins evaluated possessed anti-protozoal activity; however, this activity did not lead to methane reduction. Fenugreek saponins seemed to have potential for increasing rumen efficiency. The saponins altered the microbial community towards proliferation of fibre-degrading bacteria and inhibition of fungal population. SIGNIFICANCE AND IMPACT OF THE STUDY: The uni-directional relationship between protozoal numbers and methanogenesis, as affected by saponins, is not obligatory. All saponins might not hold promise for decreasing methane production from ruminants.

Coupling of abiotic and biotic parameters to evaluate performance of combining natural lagooning and use of two sand filters in the treatment of landfill leachates.

A study in the Etueffont landfill, located in Belfort (France), was conducted to evaluate the performance of combining natural lagooning and use of two sand filters for treating leachates through the coupling estimation of several abiotic and biotic parameters. Two gravel filters were installed in the upstream of the first basin which communicates with the remaing 2, 3 and 4 basins. The distribution of physical-chemical (T, pH, Eh, EC, O2, SM, SO4(2-), Cl-, Zn, Fe, Mg, Ni, Al, As, Ba, Cu, Sn, Zn, BOD, COD, KN, NH4+, NO2+ ,TP, AOX: absorbable organic halides, VFA: volatile fatty acids, and atrazine) and biological (bacteria, protozoa, phytoplankton) parameters was assessed in the leachate entering in basin 1, and downstream of the filters. The results showed slight variations in the physical-chemical composition of the leachate between 1999 and 2000, most likely ascribed to the maturation of the landfill but a very significant removal of SM (suspended matter) by the sand filters. This, applied to the majority of the studied parameters. Thus, the sand filter treatment of the leachates combined with natural lagooning was efficient in the improvement of water clarification.

Phosphorus and nitrate removal by selected wastewater protozoa isolates.

In the present study, the efficiency often selected wastewater protozoa in the removal of phosphorus and nitrogen and their effects on other physico-chemical parameters was investigated. Protozoa were isolated from the aerobic zone of Daasport wastewater treatment plant, in Pretoria, South Africa, using the modified Chalkey's medium. The isolates were screened for nutrient removal ability in shake flasks, at laboratory temperatures for 96 h. During each sampling, aliquot samples were collected for the analysis of phosphorus, nitrate-nitrogen, Chemical Oxygen Demand (COD), Dissolved Oxygen (DO), pH, of the mixed liquor including the growth rate of the isolates using standard methods. The results indicated a steady increase in growth rate of the isolates and all the isolates used in this study showed some measure of phosphorus and nitrate removal ability. In the presence of the test protozoa isolates, an increase in COD and a decrease in DO were noted in the mixed liquor inoculated with the organisms, while the pH only increases slightly. This study revealed a significant correlation between growth rate and nutrient removal (R = -0.806, p < 0.001 for phosphorus; R = -0.799, p < 0.01 for nitrate). The present study has been able to show that certain protozoa isolates have the ability to biologically remove phosphorus and nitrate from effluent. Consequently, it would be necessary to identify what strains of protozoa are capable of excess phosphorus and nitrogen uptake for the treatment of wastewater.

A new labyrinthulid isolate that produces only docosahexaenoic acid.

We show here that a new labyrinthulid strain, L72, isolated from a fallen leaf in the Seto Inland Sea of Japan, produced only docohexaenoic acid (DHA) among all the long-chain polyunsaturated fatty acids (LCPUFAs). The main fatty acid composition was 16:0 (28.9%), 18:0 (7.2%), 18:1 (5.7%), 18:2 (10.4%), and DHA (45.9%) without any other LCPUFA. The lipid content of the strain was 27.4%. The cells had many lipid bodies, which were densely located in all of the cells. On phylogenetic analysis using the 18S rDNA sequence, the strain was located in the labyrinthulids group, forming a monophyletic group with Labyrinthula sp. (strain s) and Labyrinthuila sp. (strain L59). We further tested the culture optimization of strain L72 to evaluate the ability of the strain to produce DHA. The optimum salt concentration and the temperature of the strain were 100% of artificial seawater and 20 degrees C. Strain L72 could grow well on soybean oil (SBO) or soybean lecithin (SBL) as the carbon source. When 20 g/l of SBL was added to the medium, DHA production reached the maximum amount at 0.67 g/l for 14 d. The two important facts, that the strain can use SBL as the main nutrient and contains only DHA among the LCPUFAs, will be of great advantage for industry.

Phytophthora tropicalis on Hedera helix and Epipremnum aureum in Polish greenhouses.

Phytophthora tropicalis was isolated from Hedera helix and Epipremnum aureum showing discoloration of leaves, necrosis of shoot base, spread upwards and on roots. The species was detected from 7/8 plants of Hedera and 3/4 of Epipremnum. Additionally Botrytis cinerea, Fusarium avenaceum and Rhizoctonia solani were recovered from some of diseased plants. P. tropicalis caused leaf necrosis of 13 plant species and tomato seedlings. The quickest spread of necrosis was observed on leaves of Peperomia magnoliaefolia, Pelargonium zonale and Phalaenopsis x hybridum. The disease developed at temperature ranged from 10 degrees to 32.5 degrees C with optimum 30 degrees C.

Characterisation of the behaviour of particles in biofilters for pre-treatment of drinking water.

Biofiltration of surface water was examined using granular activated carbon (GAC) and expanded clay (EC). Particle removal was 60-90%, measured by flow cytometry, which enabled discrimination between total- and autofluorescent particles (microalgae) in size ranges of 0.4-1 and 1-15 microm, and measured by on-line particle counting. Total particles were removed at a higher degree than autofluorescent particles. The biofilters were also challenged with 1 microm fluorescent microspheres with hydrophobic and hydrophilic surface characteristics and bacteriophages (Salmonella typhimurium 28B). Added microspheres were removed at 97-99% (hydrophobic) and 85-89% (hydrophilic) after 5 hydraulic residence times (HRT) and microspheres retained in the biofilter media were slowly detaching into the filtrate for a long time after the addition. Removal of bacteriophages (5 HRT) was considerably lower at 40-59%, and no long-lasting detachment was observed. A comparison of experimental data with theoretical predictions for removal of particles in clean granular media filters revealed a similar or higher removal of particles around 1 microm in size than predicted, while bacteriophages were removed at a similar or lesser extent than predicted. The results highlight the selectivity and dynamic behaviour of the particle removal processes and have implications for operation and microbial risk assessment of a treatment train with biofilters as pre-treatment.

Influence of top-down and bottom-up manipulations on the R-BT065 subcluster of beta-proteobacteria, an abundant group in bacterioplankton of a freshwater reservoir.

We studied the effects of nutrient availability and protistan grazing on bacterial dynamics and community composition (BCC) in different parts of the canyon-shaped Rímov reservoir (Czech Republic). The effects of protistan grazing on BCC were examined using a size fractionation approach. Water from the dam area with only bacteria (<0.8 microm), bacteria and heterotrophic nanoflagellates (<5 microm), or whole water were incubated in situ inside dialysis bags. Top-down or predator manipulations (size fractionation) were also combined with bottom-up or resource manipulations, i.e., transplantation of samples to the middle and upper inflow parts of the reservoir with increased phosphorus availability. Significant genotypic shifts in BCC occurred with transplantation as indicated by denaturing gradient gel electrophoresis. Using different probes for fluorescence in situ hybridization, we found that 10 to 50% of total bacteria were members of the phylogenetically small cluster of beta-proteobacteria (targeted with the probe R-BT065). These rod-shaped cells of very uniform size were vulnerable to predation but very fast growing and responded markedly to the different experimental manipulations. In all the grazer-free treatments, the members of the R-BT065 cluster showed the highest net growth rates of all studied bacterial groups. Moreover, their relative abundance was highly correlated with bacterial bulk parameters and proportions of bacteria with high nucleic acid (HNA) content. In contrast, increasing protistan bacterivory yielded lower proportions of R-BT065-positive and HNA bacteria substituted by increasing proportions of the class Actinobacteria, which profited from the enhanced protistan bacterivory.

A combination of soft-shell turtle powder and essential oil of a unicellular chorophyte prevents bone loss and decreased bone strength in ovariectomized rats.

The effects of soft-shell turtle (Trionyx sinensis) powder (SST) on the proximal tibiae of ovariectomized (OVX) rats were investigated using peripheral quantitative computed tomography (pQCT) and examination of serum biochemical markers. Considering the relationship between the antioxidative property and antiosteoporotic activity, the synergistic effects of a mixture of SST and essential oil of the microalgae Haematococcus pluvialis (OHP) with strong antioxidant activity were also examined. Oral administration of SST (100, 200 mg/kg) or a mixture of SST (100, 200 mg/kg) and OHP (13, 26 mg/kg) three times weekly prevented the decrease in bone mineral content (BMC) in total bone, BMC and bone mineral density (BMD) in cortical bone, and bone strength indices induced by ovariectomy in a dose-dependent manner without uterine side effects. However, OHP alone showed no significant effects.

[Initiation of self-organization processes in community of marine microbenthos by application of nutrients in super-high concentrations]. / Initsiirovanie protsessov samoorganizatsii v soobshchestve morskogo mikrobentosa sverkhvysokimi kontsentratsiiami biogennykh élementov.

The influence of high concentrations of mineral nitrogen, phosphorus and their mixtures on species structure of microbenthos of a sand intertidal zone of the White Sea was studies in field experiment. The increase in concentration of nutrients (in comparison with natural) reduces the species diversity and organism abundance in grazing chains, but stimulates the development of organisms of detrital food chain. At abnormally high concentration of nutrients the response of community does not strictly depend on chemical composition of fertilizers and N:P atomic ratio. The high concentration of nutrients act as distructive agent on the complex organized system and simultaneously as a specific trigger of self organization processes, which re resulted in formation of highly coherent commynity of r-strategists (bacteria and protists). After termination of the experiment and resetting of environment to the previous state, the new community for a long time (measured by dozens of generations of unicellular organisms) retains its structure.

Improving the effluent of small wastewater treatment plants by bacteria reduction and nutrient removal with an algal biofilm.

In wastewater ponds, bacteria numbers decrease considerably in the case of raised algae concentrations in the effluent. This shows that algae have a high potential for bacteria reduction in wastewater. Simultaneously, algae remove nutrients from the water for the formation of biomass. However, suspended algae also cause a high secondary pollution in the effluent of wastewater treatment plants. By using attached algae, as they are frequently observed as an algal biofilm in the effluent of wastewater treatment plants, the problem of separation of algae and water can be avoided. Furthermore, the algae can be removed simply from the water. In this study the possibilities for bacteria reduction and nutrient removal were examined with the aid of an algal biofilm. The results show that an algal biofilm process can be used for cases where small amounts of wastewater should be treated and a high quality of the effluent should be attained.

Contaminantes poco habituales en extendidos de esputos / Uncommon contaminants of sputum smears

Planteamiento: Describir una serie de contaminantes a través de la observación microscópica de extendidos citológicos de esputos. Material y métodos: Extendidos de esputos coloreados mediante la técnica de Papanicolaou. Resultados: Hemos constatado, en 15.000 muestras de pacientes ingresados con diferentes patologías respiratorias durante los últimos 10 años, la presencia de diferentes tipos de microalgas, células vegetales, granos de polen y diversos cristales. Conclusiones: La existencia de contaminantes, en extendidos de esputos, es un hecho relativamente frecuente, teniendo un cierto significado biológico y debiéndose establecer en ocasiones su diagnóstico diferencial, dadas las similitudes con otras estructuras tales como hongos y diversos protozoos (AU)